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Previous efforts have been made to identify marker genes that can resolve closely related organisms. Protein-coding marker genes which are rarely horizontally transferred and exist in single copies within genomes have been identified [1]. These include a set of 40 marker genes [2,3] and 107 marker genes [3].

Marker genes are commonly used in taxonomic profiling of environmental samples to identify gene families. These genes are also used in phylogenetic inference to reconstruct the evolutionary history of organisms.

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A Dummies’ Intro to Bioinformatics The word Bioinformatics is making quite a turnaround in today’s world of Science. The word seems to be made up of two…towardsdatascience.com

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In bacterial cells, single-copy marker genes are expected to occur once. In other words, each bacterial cell contains only one copy of each of these single-copy marker genes. These genes are essential for the life-functions and can be found in the majority of the bacterial species.

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When we think of the word marker, the first thing that comes to our minds is something that is used to indicate a place. For example, it can be your current location on Google Maps or it can be the place where you planted some seeds in your garden. Similarly, in genomics studies, we can find marker genes in bacterial genomes. In this article, I will introduce you to marker genes used in metagenomics analysis, how they are used and walk you through an example of a commonly used gene prediction tool.

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A Dummies’ Intro to Bioinformatics The word Bioinformatics is making quite a turnaround in today’s world of Science. The word seems to be made up of two…towardsdatascience.com

Marker genes have become a very powerful aspect in bioinformatics research which has allowed researchers to gain insights into the taxonomic information and evolutionary history of bacterial and archaeal species. The field of metagenomics benefits immensely from studies based on marker genes.

Recently, reference-free binning tools such as MaxBin and SolidBin have used single-copy marker genes to identify the number of species in a given sample. Moreover, tools such as MyCC use single-copy marker genes to refine resulting clusters.

[3] Wu D, Jospin G, Eisen JA (2013) Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups. PLoS ONE 8(10): e77033. https://doi.org/10.1371/journal.pone.0077033